Gordon. The ending of TDK just slays me every time 'Stop pointing that gun at my family!'. Brilliant stuff, and a great representation of Jim as he is in the comics.

__________________Bruce Wayne: [while on a boat surrounded by beautiful Russian ballerinas] You going to be all right Alfred? Alfred Pennyworth: [beat] You can tell them the Russian for "apply your own bloody suntan lotion."

Eh, kind of difficult to give a straightforward list, given how some of those characters can't even compete against each other (i.e. one being more about over-the-top performance, the other a relatable everyman etc.)... Bane is mostly a performance and a presence than a character, while the other big "larger than life freak", the Joker, is already more of a personality. Jonathan Crane (the BB one) probably takes the cake as the "normal" kind of cold-eyed villain, followed closely by Stryver, and... well, no one left in that category except those creepy LoS extras from BB
Falcone > Maroni in terms of semi-comedic mobster charm, the Chechen is a unique ethnic caricature and also in his own category, and Flass the dirty bastard can't really be compared to anyone either.
Then we haev the slightly comical "camp" blokes: the CIA agent's the best, then Daggett, and... wait who else?

Among the good guys, Catwoman and Bruce Wayne are the ones providing the theatralic comedy... she is awesome half the time and kind of awkward otherwise, he's completely awesome but only has few scenes in that character. So he'd be number one then?
Batman, the OTT version, starts out really cool, but then start becoming corny at the very end of TDK, and then it only gets worse. Where to place him?

Bruce Wayne himself morphs between charismatic, stoic and slightly dull, no idea - and Harvey Dent is a unique case of a character morphing from relatable and human into over-the-top. Guess they're about equal? Blake may be equal to Dent before he turns evil / starts showing his darker side in terms of being the sympathetic nice guy, although not sure if he get to do all that much otherwise...

I like all of them. It's really hard to choose the one. I was chose Bruce. In this trilogy we were watched Bruce's ups and downs. We saw how complex is this character.
But if I will have to choose the best villain I will take Bane.